Limits...
Efficient detection of QTL with large effects in a simulated pig-type pedigree using selective genotyping.

Heuven HC, Bastiaansen JW, van den Berg SM - BMC Proc (2009)

Bottom Line: Four additional QTL with small effects were found in the second stage.The two-stage genotyping strategy with selective genotyping detected regions with highly significant QTL useful for further fine-mapping.The large reduction in costs allows for follow-up expression and functional studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, P,O, box 80163, 3508 TD Utrecht, The Netherlands. h.c.m.heuven@uu.nl

ABSTRACT

Background: The ultimate goal of QTL studies is to find causative mutations, which requires additional expression studies. Given the limited amount of time and funds, the smart option is to identify the most important QTL with minimal effort. A cost-effective solution is to genotype only those animals with high or low phenotypic values or DNA-pools of these individuals. A two-stage genotyping strategy was applied on samples in the tails of the distribution of breeding values.

Results: The tail-analysis approach identified eight out of the 19 QTL in the first stage, explaining about half of 98% of the genetic variance. Four additional QTL with small effects were found in the second stage.

Conclusion: The two-stage genotyping strategy with selective genotyping detected regions with highly significant QTL useful for further fine-mapping. The large reduction in costs allows for follow-up expression and functional studies.

No MeSH data available.


Likelihood ratio profiles for chromosomes 1, 2, 3 and 4 with adjusted threshold.
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Figure 1: Likelihood ratio profiles for chromosomes 1, 2, 3 and 4 with adjusted threshold.

Mentions: Subsequently LDLA was applied to these 114 markers and the profiles of the likelihood ratio test are shown in Figure 1 for chromosomes 1, 2, 3, and 4. Given these graphs and results from Table 3, two QTL are expected on chromosome 1, one QTL on chromosome 2, three or four QTL on chromosome 4 and none on chromosomes 3, 5, and 6.


Efficient detection of QTL with large effects in a simulated pig-type pedigree using selective genotyping.

Heuven HC, Bastiaansen JW, van den Berg SM - BMC Proc (2009)

Likelihood ratio profiles for chromosomes 1, 2, 3 and 4 with adjusted threshold.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2654502&req=5

Figure 1: Likelihood ratio profiles for chromosomes 1, 2, 3 and 4 with adjusted threshold.
Mentions: Subsequently LDLA was applied to these 114 markers and the profiles of the likelihood ratio test are shown in Figure 1 for chromosomes 1, 2, 3, and 4. Given these graphs and results from Table 3, two QTL are expected on chromosome 1, one QTL on chromosome 2, three or four QTL on chromosome 4 and none on chromosomes 3, 5, and 6.

Bottom Line: Four additional QTL with small effects were found in the second stage.The two-stage genotyping strategy with selective genotyping detected regions with highly significant QTL useful for further fine-mapping.The large reduction in costs allows for follow-up expression and functional studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, P,O, box 80163, 3508 TD Utrecht, The Netherlands. h.c.m.heuven@uu.nl

ABSTRACT

Background: The ultimate goal of QTL studies is to find causative mutations, which requires additional expression studies. Given the limited amount of time and funds, the smart option is to identify the most important QTL with minimal effort. A cost-effective solution is to genotype only those animals with high or low phenotypic values or DNA-pools of these individuals. A two-stage genotyping strategy was applied on samples in the tails of the distribution of breeding values.

Results: The tail-analysis approach identified eight out of the 19 QTL in the first stage, explaining about half of 98% of the genetic variance. Four additional QTL with small effects were found in the second stage.

Conclusion: The two-stage genotyping strategy with selective genotyping detected regions with highly significant QTL useful for further fine-mapping. The large reduction in costs allows for follow-up expression and functional studies.

No MeSH data available.